Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.ImportanceTo fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available

Exploiting Query’s Temporal Patterns for Query Autocompletion

Query autocompletion (QAC) is a common interactive feature of web search engines. It aims at assisting users to formulate queries and avoiding spelling mistakes by presenting them with a list of query completions as soon as they start typing in the search box. Existing QAC models mostly rank the query completions by their past popularity collected in the query logs. For some queries, their popularity exhibits relatively stable or periodic behavior while others may experience a sudden rise in their query popularity. Current time-sensitive QAC models focus on either periodicity or recency and are unable to respond swiftly to such sudden rise, resulting in a less optimal QAC performance. In this paper, we propose a hybrid QAC model that considers two temporal patterns of query’s popularity, that is, periodicity and burst trend. In detail, we first employ the Discrete Fourier Transform (DFT) to identify the periodicity of a query’s popularity, by which we forecast its future popularity. Then the burst trend of query’s popularity is detected and incorporated into the hybrid model with its cyclic behavior. Extensive experiments on a large, real-world query log dataset infer that modeling the temporal patterns of query popularity in the form of its periodicity and its burst trend can significantly improve the effectiveness of ranking query completions

Impaired Functional Criticality of Human Brain during Alzheimer's Disease Progression

The progression of Alzheimer's Disease (AD) has been proposed to comprise three stages, subjective cognitive decline (SCD), mild cognitive impairment (MCI), and AD. Was brain dynamics across the three stages smooth? Was there a critical transition? How could we characterize and study functional criticality of human brain? Based on dynamical characteristics of critical transition from nonlinear dynamics, we proposed a vertex-wise Index of Functional Criticality (vIFC) of fMRI time series in this study. Using 42 SCD, 67 amnestic MCI (aMCI), 34 AD patients as well as their age-, sex-, years of education-matched 54 NC, our new method vIFC successfully detected significant patient-normal differences for SCD and aMCI, as well as significant negative correlates of vIFC in the right middle temporal gyrus with total scores of Montreal Cognitive Assessment (MoCA) in SCD. In comparison, standard deviation of fMRI time series only detected significant differences between AD patients and normal controls. As an index of functional criticality of human brain derived from nonlinear dynamics, vIFC could serve as a sensitive neuroimaging marker for future studies; considering much more vIFC impairments in aMCI compared to SCD and AD, our study indicated aMCI as a critical stage across AD progression

Isolated splenic metastasis from primary fallopian tube carcinoma and the application of laparoscopic splenectomy: a case report and literature review

Metastases to the spleen from various non-hematologic malignancies are generally not a common clinical event and usually indicate the late dissemination of disease. Solitary splenic metastases from solid neoplasm are extremely uncommon. Furthermore, solitary metastasis to the spleen from primary fallopian tube carcinoma (PFTC) is extremely rare and has not been reported previously. We report a case of isolated splenic metastasis in a 60-year-old woman, occurring 13 months after a total hysterectomy, a bilateral salpingo-oophorectomy, a pelvic lymphadenectomy, a para-aortic lymphadenectomy, an omentectomy, and an appendectomy were performed for PFTC. The patient’s serum tumor marker CA125 was elevated to 49.25 U/ml (N < 35.0 U/ml). An abdominal computed tomography (CT) scan revealed a 4.0 × 3.0 cm low-density lesion in the spleen that was potentially malignant, with no lymphadenectasis or distant metastasis. The patient underwent a laparoscopic exploration, and one lesion was found in the spleen. Then, a laparoscopic splenectomy (LS) confirmed a splenic metastasis from PFTC. The histopathological diagnosis showed that the splenic lesion was a high-differentiated serous carcinoma from PFTC metastasis. The patient recovered for over 1 year, with no tumor recurrence. This is the first reported case of an isolated splenic metastasis from PFTC. This case underlines the importance of serum tumor marker assessment, medical imaging examination, and history of malignancy during follow-up, and LS seems to be the optimal approach for isolated splenic metastasis from PFTC

A High speed, high bandwidth Versatile DAS for breast cancer detection

The data acquisition system (DAS) developed aims to get the 3D breast cancer tomography with 8 current injection channels and 117 voltage measurement channels, capable of generating and measuring voltages and currents. By adopting special electrode and careful circuit layout, the initial bandwidth without calibration can reach 5 MHz. Electrical test results show that the system has a SNR greater than 67dB at 5MHz without digital enhancement method

The Optimal Axial Anatomical Site for a Single-Slice Area to Quantify the Total Volume of Visceral Adipose Tissue in Quantitative CT

PurposeDetermine the association between cross-sectional visceral adipose tissue (VAT) area of different anatomic locations and total abdominopelvic VAT volume; identify the optimal measurement site in a single-slice to quantify the total VAT volume.MethodParticipants who underwent non-contrast abdominal scan by quantitative CT (QCT) were enrolled from May 2021 to October 2021. The VAT area (cm2) at different anatomic sites as upper-pole, lower-pole, and hilum of the kidney, intervertebral disc of L2/L3 and L5/S1, and umbilical level were measured on QCT PRO BMD workstation (Mindways QCT PRO workstation). The total VAT volume (cm3) from the upper pole of kidney to the L5/S1 intervertebral disc of the pelvis (abdominopelvic region) was obtained by using Siemens Healthineers Syngo via Frontier cardiac risk assessment. Regression models were used to identify the optimal single-slice in different gender for estimating VAT volume. Statistical significance was established at P < 0.05.ResultsTotal of 311 Chinese participants including 179 men [age, 55.1 ± 14.9 years; body mass index (BMI), 24.2 ± 3.2 kg/m2; total VAT volume, 2482.6 ± 1276.5 mL] and 132 women [age, 54.3 ± 14.9; BMI, 23.5 ± 2.9; total VAT volume, 1761.5 ± 876.4]. Pearson’s correlation analysis revealed a strong association between the VAT area and total abdominopelvic VAT volume at the hilum of the kidney in both men (r=0.938, P<0.001) and women (r=0.916, P<0.001). Adjust for covariates including age, BMI, and waist circumference make a relatively small effect on predicting the total VAT volume.ConclusionsMeasurement of cross-sectional areas at the hilum of the kidney in both genders showed a strongest relation to TVAT volume. Our results may provide an identifiable and valuable axial landmark for measuring visceral adipose tissue in clinical practice

Unraveling the transcriptome-based network of tfh cells in primary sjogren syndrome: insights from a systems biology approach

BackgroundPrimary Sjogren Syndrome (pSS) is an autoimmune disease characterized by immune cell infiltration. While the presence of follicular T helper (Tfh) cells in the glandular microenvironment has been observed, their biological functions and clinical significance remain poorly understood.MethodsWe enrolled a total of 106 patients with pSS and 46 patients without pSS for this study. Clinical data and labial salivary gland (LSG) biopsies were collected from all participants. Histological staining was performed to assess the distribution of Tfh cells and B cells. Transcriptome analysis using RNA-sequencing (RNA-seq) was conducted on 56 patients with pSS and 26 patients without pSS to uncover the underlying molecular mechanisms of Tfh cells. To categorize patients, we employed the single-sample gene set enrichment analysis (ssGSEA) algorithm, dividing them into low- and high-Tfh groups. We then utilized gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), and deconvolution tools to explore functional and immune infiltration differences between the low- and high-Tfh groups.ResultsPatients with pSS had a higher positive rate of the antinuclear antibody (ANA), anti-Ro52, anti-SSA, anti-SSB and hypergammaglobulinaemia and higher levels of serum IgG compared to the non-pSS. Histopathologic analyses revealed the presence of Tfh cells (CD4+CXCR5+ICOS+) in germinal centers (GC) within the labial glands of pSS patients. GSEA, WGCNA, and correlation analysis indicated that the high-Tfh group was associated with an immune response related to virus-mediated IFN response and metabolic processes, primarily characterized by hypoxia, elevated glycolysis, and oxidative phosphorylation levels. In pSS, most immune cell types exhibited significantly higher infiltration levels in the high-Tfh group compared to the low-Tfh group. Additionally, patients in the Tfh-high group demonstrated a higher positive rate of the ANA, rheumatoid factor (RF), and hypergammaglobulinaemia, as well as higher serum IgG levels.ConclusionOur study suggests that Tfh cells may play a crucial role in the pathogenesis of pSS and could serve as potential therapeutic targets in pSS patients

Characterisation of macrophage infiltration and polarisation based on integrated transcriptomic and histological analyses in Primary Sjögren’s syndrome

BackgroundPrimary Sjögren’s syndrome (pSS) is a progressive inflammatory autoimmune disease. Immune cell infiltration into glandular lobules and ducts and glandular destruction are the pathophysiological hallmarks of pSS. Macrophages are one of the most important cells involved in the induction and regulation of an inflammatory microenvironment. Although studies have reported that an abnormal tissue microenvironment alters the metabolic reprogramming and polarisation status of macrophages, the mechanisms driving macrophage infiltration and polarisation in pSS remain unclear.MethodsImmune cell subsets were characterised using the single-cell RNA sequencing (scRNA-seq) data of peripheral blood mononuclear cells (PBMCs) from patients with pSS (n = 5) and healthy individuals (n = 5) in a public dataset. To evaluate macrophage infiltration and polarisation in target tissues, labial salivary gland biopsy tissues were subjected to histological staining and bulk RNA-seq (pSS samples, n = 24; non-pSS samples, n = 12). RNA-seq data were analysed for the construction of macrophage co-expression modules, enrichment of biological processes and deconvolution-based screening of immune cell types.ResultsDetailed mapping of PBMCs using scRNA-seq revealed five major immune cell subsets in pSS, namely, T cells, B cells, natural killer (NK) cells, dendritic cells (DCs) and monocyte-macrophages. The monocyte-macrophage subset was large and had strong inflammatory gene signatures. This subset was found to play an important role in the generation of reactive oxygen species and communicate with other innate and adaptive immune cells. Histological staining revealed that the number of tissue-resident macrophages was high in damaged glandular tissues, with the cells persistently surrounding the tissues. Analysis of RNA-seq data using multiple algorithms demonstrated that the high abundance of pro-inflammatory M1 macrophages was accompanied by the high abundance of other infiltrating immune cells, senescence-associated secretory phenotype and evident metabolic reprogramming.ConclusionMacrophages are among the most abundant innate immune cells in PBMCs and glandular tissues in patients with pSS. A bidirectional relationship exists between macrophage polarisation and the inflammatory microenvironment, which may serve as a therapeutic target for pSS